Results for 2017 campaign
PhD Chapter 1 (Part 3/4)
This series of files compile all analyses done during Chapter 1 (analyses_1, analyses_2, analyses_cartography, kriging), with a division by campaign (2014, 2016 and 2017).
To navigate on this page:
- Click on the table of contents in the left margin to assess sections
- Click on a figure to zoom it
- Click here to go directly to the graphical explorations
- Click here to go directly to the analyses
Details about softwares and files used:
- Files: Chap1_article_2014.Rmd, Chap1_article_2016.Rmd, Chap1_article_2017.Rmd, Chap1_article_GIS.Rmd, Chap1_functions.R, Chap1_data_import.R
- Archive Folder: Wumpa Pro/DOCTORAT/ANALYSES/Chap1
- PRIMER version: 6
- R version: 3.5
To return to Chapter 1’s index page, click here.
Workspace preparation
setwd("Documents/PROJECTS/Chap1")
# Needed if working with Parallels Desktop
.libPaths("C:/Users/eldre/Documents/R/win-library/3.5")Loading of the packages
Loading of the datasets
Here, we use data from subtidal ecosystems (see metadata files for more information)
Only stations that have been sampled both for abiotic parameters and benthic species were included.
Note that the sieving method is not the same between campaigns: 2014 and 2017 campaigns used 500µm sieves and 2016 used 1000µm sieves.
The script below includes personnal functions, refined data, parameters for each campaign and global means, sd, se.
Also includes heavy metals concentrations for campaign 2017 obtained after inverse weighting distance kriging (see data_creation script).
Selected variables are:
- depth of the station: depth
- percentage of organic matter: om
- percentage of gravel: gravel
- percentage of sand: sand
- percentage of silt: silt
- percentage of clay: clay
- concentration of arsenic: arsenic
- concentration of cadmium: cadmium
- concentration of chromium: chromium
- concentration of copper: copper
- concentration of iron: iron
- concentration of manganese: manganese
- concentration of mercury: mercury
- concentration of lead: lead
- concentration of zinc: zinc
- species richness: S
- abundance of total species individuals: N
- Shannon index: H
- Piélou evenness: J
- abundance of Bipalponephtys neotena: Bneo
- abundance of Macoma calcarea: Mcal
- abundance of Echinarachinus parma: Epar
- abundance of Nematoda: Nema
Species were selected using the IndVal calculation and SIMPER procedure in PRIMER, and correlations between parameters were checked (see below).
As there is not the same number of replicates for metal concentrations and the rest of the variables, two sets of data have been produced: one with all stations available for each analysis (full dataset), and one with stations only at BSI (reduced dataset).
Graphical explorations
1. Parameters
Here are the barlots for the values of each selected variable at each BSI and MR stations. Barplots have been created with the full datasets.
Results of univariate PermANOVAs on parameters and multivariate PermANOVA on the whole benthic community (PRIMER)
| Variable | Region | Comments |
|---|---|---|
| depth | ||
| om | S | |
| gravel | ||
| sand | S | |
| silt | S | |
| clay | ||
| Bneo (500 µm) | S | |
| Mcal (500 µm) | S | |
| Epar (500 µm) | S | |
| Nema (500 µm) | S | |
| S (500 µm) | S | |
| N (500 µm) | ||
| H (500 µm) | ||
| J (500 µm) | ||
| ALL SPECIES (500 µm) | S | |
| Bneo (1 mm) | S | |
| Mcal (1 mm) | S | |
| Epar (1 mm) | S | |
| Nema (1 mm) | S | |
| S (1 mm) | S | |
| N (1 mm) | ||
| H (1 mm) | ||
| J (1 mm) | ||
| ALL SPECIES (1 mm) | S |
Depth
## Performing barplot for: mean (legend is: depth )
Organic matter
## Performing barplot for: mean (legend is: om )
Grain-size
## Using group as id variables
## Performing barplot for: mean (legend is: gravel )
## Performing barplot for: mean (legend is: sand )
## Performing barplot for: mean (legend is: silt )
## Performing barplot for: mean (legend is: clay )
Heavy-metals
This section is not relevant here, as we only have data for BSI.
Species abundances
## Using group as id variables
## Performing barplot for: mean (legend is: Bneo )
## Performing barplot for: mean (legend is: Mcal )
## Performing barplot for: mean (legend is: Epar )
## Performing barplot for: mean (legend is: Nema )
Diversity indices
## Using group as id variables
## Performing barplot for: mean (legend is: S )
## Performing barplot for: mean (legend is: N )
## Performing barplot for: mean (legend is: H )
## Performing barplot for: mean (legend is: J )
2. Phylum frequencies
Phylum frequencies have been calculated with the full datasets.
3. Species estimation curves
Accumulation and rarefaction curves have been calculated with the full datasets.
4. Principal Component Analysis
All abiotic variables at BSI
Variables have been scaled by mean and standard-deviation prior to analysis.
Parameters
Variables have been scaled by mean and standard-deviation prior to analysis.
Metals at BSI
Variables have been scaled by mean and standard-deviation prior to analysis.
5. Non-metric Multidimensional Scaling
All abiotic parameters at BSI
Variables have been scaled by mean and standard-deviation prior to analysis.
Parameters
Variables have been scaled by mean and standard-deviation prior to analysis.
Metals at BSI
Variables have been scaled by mean and standard-deviation prior to analysis.
Species
Stations with no species are deleted from this analysis.
6. Hierarchical Agglomerative Clustering
All abiotic variables at BSI
Variables have been scaled by mean and standard-deviation prior to analysis.
## 127 128 129 130 131 132 134 135 136 137 138 139 140 141 142 143 144 145
## 1 1 1 2 1 1 1 1 1 1 3 3 1 1 1 1 1 1
## 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163
## 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2
## 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181
## 2 2 3 3 4 3 3 3 3 4 4 4 4 4 4 4 4 4
## 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
## 4 3 3 4 4 3 1 2 2 2 2 1 1 3 2 2 3 1
## 200 201 202 203 204 205 206 207 208 209 211 212 214 215 216 217 218 219
## 2 2 3 3 4 4 4 4 4 1 4 4 4 1 2 3 1 2
## 220 221 222 223 224 225 226 228 229 230 231 232 233 234 235 236 237 238
## 3 4 4 4 4 4 4 1 2 3 1 3 3 3 4 4 3 2
## 239 240 241
## 2 1 2
## Warning in rm(hac_spec17, groups1): objet 'hac_spec17' introuvable
Parameters
Variables have been scaled by mean and standard-deviation prior to analysis.
## 127 128 129 130 131 132 134 135 136 137 138 139 140 141 142 143 144 145
## 1 2 3 4 2 2 2 2 2 2 3 1 1 2 2 2 3 2
## 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163
## 2 2 2 2 2 2 1 1 1 1 1 1 1 1 4 1 1 1
## 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181
## 1 1 4 4 1 4 4 4 4 1 1 1 1 1 1 1 1 1
## 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
## 1 3 4 1 1 4 1 1 1 1 1 1 2 4 1 1 4 2
## 200 201 202 203 204 205 206 207 208 209 211 212 214 215 216 217 218 219
## 1 1 3 4 1 1 1 1 1 3 4 4 4 3 1 4 1 4
## 220 221 222 223 224 225 226 228 229 230 231 232 233 234 235 236 237 238
## 1 1 4 4 4 4 1 1 1 4 1 4 4 4 1 1 3 1
## 239 240 241 243 246 248 249 251 252 254 255 257 258 260 261 264 267 270
## 1 2 1 3 4 4 3 4 3 4 4 4 4 4 4 4 4 4
Metals at BSI
Variables have been scaled by mean and standard-deviation prior to analysis.
## 127 128 129 130 131 132 134 135 136 137 138 139 140 141 142 143 144 145
## 1 1 1 1 2 2 1 1 1 1 1 3 1 1 1 1 1 1
## 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163
## 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
## 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181
## 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
## 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
## 3 3 3 3 3 2 2 2 2 2 2 2 3 3 2 2 3 2
## 200 201 202 203 204 205 206 207 208 209 211 212 214 215 216 217 218 219
## 2 2 3 3 3 3 3 3 3 2 3 3 3 2 2 3 2 2
## 220 221 222 223 224 225 226 228 229 230 231 232 233 234 235 236 237 238
## 3 3 3 3 3 3 3 1 3 3 1 3 3 3 3 3 3 2
## 239 240 241
## 2 2 2
Species
## 127 128 129 130 131 132 134 135 136 137 138 139 140 141 142 143 144 145
## 1 2 2 1 2 2 2 2 2 2 2 1 2 2 2 2 2 2
## 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163
## 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1
## 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181
## 2 2 1 1 2 1 1 1 1 1 2 1 2 2 2 2 2 2
## 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
## 2 2 1 2 2 1 1 2 1 2 2 1 1 1 2 2 1 2
## 200 201 202 203 204 205 206 207 208 209 211 212 214 215 216 217 218 219
## 2 2 1 2 1 2 1 2 2 1 2 1 2 1 1 1 2 1
## 220 221 222 223 224 225 226 228 229 230 231 232 233 234 235 236 237 238
## 1 2 2 2 1 2 2 1 2 1 2 1 1 1 1 2 1 1
## 239 240 241 243 246 248 249 251 252 254 255 257 258 260 261 264 267 270
## 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Analyses
1. Correlations between parameters
Correlations between habitat and metal variables have been done with the reduced datasets only.
Parameters
| depth | om | gravel | sand | silt | clay | |
|---|---|---|---|---|---|---|
| depth | 1 | 0.311 | -0.061 | -0.142 | 0.116 | -0.117 |
| om | 0.311 | 1 | -0.361 | -0.721 | 0.741 | 0.037 |
| gravel | -0.061 | -0.361 | 1 | 0.105 | -0.407 | 0.12 |
| sand | -0.142 | -0.721 | 0.105 | 1 | -0.798 | -0.386 |
| silt | 0.116 | 0.741 | -0.407 | -0.798 | 1 | 0.087 |
| clay | -0.117 | 0.037 | 0.12 | -0.386 | 0.087 | 1 |
Metals
| arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|
| arsenic | 1 | 0.709 | 0.745 | 0.812 | 0.674 | 0.792 | 0.695 | 0.9 | 0.825 |
| cadmium | 0.709 | 1 | 0.813 | 0.698 | 0.576 | 0.751 | 0.649 | 0.819 | 0.821 |
| chromium | 0.745 | 0.813 | 1 | 0.856 | 0.824 | 0.916 | 0.623 | 0.808 | 0.891 |
| copper | 0.812 | 0.698 | 0.856 | 1 | 0.785 | 0.812 | 0.638 | 0.888 | 0.961 |
| iron | 0.674 | 0.576 | 0.824 | 0.785 | 1 | 0.863 | 0.356 | 0.614 | 0.751 |
| manganese | 0.792 | 0.751 | 0.916 | 0.812 | 0.863 | 1 | 0.544 | 0.763 | 0.807 |
| mercury | 0.695 | 0.649 | 0.623 | 0.638 | 0.356 | 0.544 | 1 | 0.816 | 0.701 |
| lead | 0.9 | 0.819 | 0.808 | 0.888 | 0.614 | 0.763 | 0.816 | 1 | 0.921 |
| zinc | 0.825 | 0.821 | 0.891 | 0.961 | 0.751 | 0.807 | 0.701 | 0.921 | 1 |
Species
| Bneo | Mcal | Epar | Nema | S | N | H | J | |
|---|---|---|---|---|---|---|---|---|
| Bneo | 1 | 0.374 | -0.382 | -0.276 | 0.467 | 0.518 | 0.215 | -0.206 |
| Mcal | 0.374 | 1 | -0.212 | 0.048 | 0.393 | 0.339 | 0.315 | -0.023 |
| Epar | -0.382 | -0.212 | 1 | 0.3 | -0.145 | -0.05 | -0.172 | -0.139 |
| Nema | -0.276 | 0.048 | 0.3 | 1 | 0.166 | 0.231 | 0.051 | -0.12 |
| S | 0.467 | 0.393 | -0.145 | 0.166 | 1 | 0.576 | 0.722 | -0.013 |
| N | 0.518 | 0.339 | -0.05 | 0.231 | 0.576 | 1 | 0.004 | -0.64 |
| H | 0.215 | 0.315 | -0.172 | 0.051 | 0.722 | 0.004 | 1 | 0.615 |
| J | -0.206 | -0.023 | -0.139 | -0.12 | -0.013 | -0.64 | 0.615 | 1 |
2. IndVal and SIMPER
These analyses allowed to select 4 species as dependant variables for the regressions. We used results from PRIMER to justify further their choice. Full datasets were used.
## cluster indicator_value probability
## bipalponephtys_neotena 1 0.7637 0.001
## macoma_calcarea 1 0.7560 0.001
## eudorellopsis_integra 1 0.5569 0.006
## protomedeia_grandimana 1 0.4054 0.036
## goniada_maculata 1 0.3694 0.024
## echinarachnius_parma 2 0.7211 0.001
## nematoda 2 0.6006 0.001
## crenella_decussata 2 0.5881 0.001
## ecrobia_truncata 2 0.3333 0.001
## phoxocephalus_holbolli 2 0.2927 0.050
## ameritella_agilis 2 0.2791 0.011
## mesodesma_arctatum 2 0.2667 0.001
## orchomenella_minuta 2 0.2145 0.013
## mysella_planulata 2 0.2000 0.002
## hiatella_arctica 2 0.1909 0.004
## parvicardium_pinnulatum 2 0.1792 0.018
## solariella_sp 2 0.1708 0.033
## ophelia_limacina 2 0.1663 0.039
## anthozoa 2 0.1276 0.022
##
## Sum of probabilities = 83.633
##
## Sum of Indicator Values = 15.21
##
## Sum of Significant Indicator Values = 7.18
##
## Number of Significant Indicators = 19
##
## Significant Indicator Distribution
##
## 1 2
## 5 14
Quitting from lines 663-673 (Chap1_article_2017.Rmd) Error in cumsum <= 0.8 : comparaison (4) possible seulement pour les types liste et atomique
3. Univariate regressions
Sand variables (Csand, Msand, Fsand) and mud variables (silt, clay) were merged to reduced the problem of model overfitting. Regressions have been splitted to include only sediment parameters or metals concentrations at a time.
All abiotic parameters at BSI
i) Simple regressions
These analyses have been do to explore the relationships between variables. As it is a huge number of results to interpret, only multiple regressions will be included in the article (see below).
| depth | om | gravel | sand | silt | clay | arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Bneo | 0.02896 | -0.004853 | -0.001284 | 0.005544 | 0.03127 | -0.003883 | 0.02658 | 0.05792 | 0.03385 | 0.05284 | -0.007023 | -0.007612 | 0.01923 | 0.06944 | 0.09318 |
| Mcal | -0.005863 | 0.02576 | -0.001422 | 0.02124 | 0.006305 | -0.00896 | 0.04531 | 0.06456 | 0.03261 | 0.004907 | -0.007508 | 0.03006 | 0.06613 | 0.06284 | 0.01137 |
| Epar | 0.01171 | 0.0884 | -0.008427 | 0.08001 | 0.05474 | -0.006003 | 0.01663 | 0.03255 | 0.0243 | 0.02964 | 0.002643 | 0.02949 | -0.005137 | 0.02621 | 0.03627 |
| Nema | -0.006172 | 0.08653 | 0.08026 | 0.02622 | 0.07877 | -0.006292 | -0.009159 | 0.002577 | -0.005425 | 0.005019 | -0.003006 | 0.003156 | 0.0006913 | 0.00456 | 0.001428 |
| S | 0.1368 | -0.009104 | -0.007717 | -0.008807 | -0.008576 | -0.00739 | 0.01662 | 0.1027 | 0.118 | 0.05078 | 0.1085 | 0.07493 | 0.002283 | 0.03525 | 0.06309 |
| N | 0.02846 | 0.02306 | -0.003185 | 0.008909 | 0.004304 | 0.0004222 | -0.006692 | -0.004822 | -0.008279 | -0.003719 | -0.001477 | -0.002075 | -0.008671 | 0.005467 | 0.005936 |
| H | 0.3053 | 0.02337 | -0.008658 | 0.00157 | -0.005121 | -0.0008101 | 0.05214 | 0.1186 | 0.1572 | 0.09365 | 0.06617 | 0.0456 | 0.00858 | 0.086 | 0.1237 |
| J | 0.1429 | 0.02409 | -0.00736 | 1.223e-05 | -0.007634 | 0.01008 | 0.06716 | 0.02249 | 0.06068 | 0.07452 | -0.00309 | -0.0007157 | 0.004781 | 0.07601 | 0.08759 |
| depth | om | gravel | sand | silt | clay | arsenic | cadmium | chromium | copper | iron | manganese | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Bneo | 0.04091 | 0.495 | 0.3561 | 0.2067 | 0.03515 | 0.4501 | 0.04787 | 0.006292 | 0.02968 | 0.008709 | 0.6304 | 0.6818 |
| Mcal | 0.5504 | 0.05056 | 0.3603 | 0.06842 | 0.1953 | 0.8792 | 0.01413 | 0.004114 | 0.03219 | 0.2169 | 0.6719 | 0.03805 |
| Epar | 0.132 | 0.0008946 | 0.7768 | 0.001532 | 0.00771 | 0.559 | 0.09367 | 0.03233 | 0.05573 | 0.03912 | 0.2583 | 0.03952 |
| Nema | 0.5697 | 0.001009 | 0.001508 | 0.04904 | 0.001659 | 0.5775 | 0.9675 | 0.2596 | 0.5251 | 0.2151 | 0.4147 | 0.2481 |
| S | 3.837e-05 | 0.9306 | 0.6922 | 0.8425 | 0.7997 | 0.6613 | 0.09373 | 0.0003555 | 0.0001322 | 0.009938 | 0.000244 | 0.002121 |
| N | 0.04227 | 0.06057 | 0.4216 | 0.1613 | 0.2271 | 0.3086 | 0.6052 | 0.4935 | 0.7563 | 0.4431 | 0.3621 | 0.3815 |
| H | 1.944e-10 | 0.0593 | 0.8138 | 0.2812 | 0.5087 | 0.342 | 0.009112 | 0.0001268 | 9.806e-06 | 0.0006383 | 0.003713 | 0.01387 |
| J | 2.554e-05 | 0.05654 | 0.6586 | 0.3192 | 0.684 | 0.1482 | 0.003486 | 0.0629 | 0.005274 | 0.002177 | 0.4179 | 0.3393 |
| mercury | lead | zinc | |
|---|---|---|---|
| Bneo | 0.0784 | 0.003012 | 0.000658 |
| Mcal | 0.003723 | 0.004594 | 0.1352 |
| Epar | 0.5096 | 0.04909 | 0.02535 |
| Nema | 0.3019 | 0.2227 | 0.2844 |
| S | 0.2657 | 0.0271 | 0.004519 |
| N | 0.8161 | 0.2079 | 0.2008 |
| H | 0.1652 | 0.001044 | 9.084e-05 |
| J | 0.219 | 0.001979 | 0.0009426 |
ii) Multiple regressions
ZIP models are “computationally” singular, so they have not been computed here.
This table is summarizing the significative relationships with all variables as predictors, obtained with the AIC-reduced models from the multiple regressions below (ZIP not included)
| Predictor | Bneo | Mcal | Epar | Nema | S | N | H | J |
|---|---|---|---|---|---|---|---|---|
| depth | - | - | + | + | - | + | + | |
| om | + | - | - | - | + | |||
| gravel | - | - | - | + | ||||
| sand | - | + | + | |||||
| silt | ||||||||
| clay | - | + | + | |||||
| arsenic | + | - | + | - | ||||
| cadmium | - | - | - | - | - | - | - | + |
| chromium | + | - | + | + | - | |||
| copper | - | - | + | - | ||||
| iron | - | - | - | - | ||||
| manganese | - | + | - | - | - | + | ||
| mercury | - | + | + | |||||
| lead | + | - | - | + | + | - | ||
| zinc | + | - | - | + | ||||
| McFadden Pseudo-R2 | 0.31 | 0.30 | 0.44 | 0.63 | ||||
| Adjusted-R2 | 0.25 | 0.09 | 0.40 | 0.30 |
Abundance of B. neotena
## FULL MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.31
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 2.86 | 0.2605 | 10.98 | 4.999e-28 | * * * |
| depth | -0.01449 | 0.001937 | -7.482 | 7.335e-14 | * * * |
| om | 0.3788 | 0.04618 | 8.203 | 2.341e-16 | * * * |
| gravel | -1.228 | 0.3515 | -3.495 | 0.0004743 | * * * |
| sand | -0.09153 | 0.2125 | -0.4308 | 0.6666 | |
| clay | -3.001 | 0.4623 | -6.491 | 8.551e-11 | * * * |
| arsenic | 0.1742 | 0.02991 | 5.825 | 5.699e-09 | * * * |
| cadmium | -19.48 | 2.387 | -8.16 | 3.344e-16 | * * * |
| chromium | 0.0194 | 0.00525 | 3.696 | 0.0002189 | * * * |
| copper | -0.1212 | 0.0256 | -4.736 | 2.179e-06 | * * * |
| iron | -2.74e-05 | 5.594e-06 | -4.898 | 9.672e-07 | * * * |
| manganese | -0.001179 | 0.0001475 | -7.995 | 1.297e-15 | * * * |
| mercury | -0.7621 | 2.702 | -0.2821 | 0.7779 | |
| lead | 0.1482 | 0.05692 | 2.603 | 0.009241 | * * |
| zinc | 0.07154 | 0.01024 | 6.984 | 2.878e-12 | * * * |
| depth | om | gravel | sand | clay | arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| VIF | 1.53 | 2.04 | 1.04 | 2.02 | 1.09 | 2.24 | 3.39 | 4.03 | 5.86 | 2.94 | 3.11 | 1.62 | 4.9 | 8.6 |
## REDUCED MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.31
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 2.776 | 0.1789 | 15.52 | 2.539e-54 | * * * |
| depth | -0.01435 | 0.001908 | -7.519 | 5.514e-14 | * * * |
| om | 0.3913 | 0.0357 | 10.96 | 6.035e-28 | * * * |
| gravel | -1.213 | 0.3499 | -3.466 | 0.0005273 | * * * |
| clay | -2.921 | 0.4192 | -6.968 | 3.209e-12 | * * * |
| arsenic | 0.176 | 0.02926 | 6.015 | 1.796e-09 | * * * |
| cadmium | -19.72 | 2.303 | -8.563 | 1.096e-17 | * * * |
| chromium | 0.01936 | 0.00524 | 3.695 | 0.0002197 | * * * |
| copper | -0.1237 | 0.02479 | -4.989 | 6.071e-07 | * * * |
| iron | -2.783e-05 | 5.404e-06 | -5.15 | 2.599e-07 | * * * |
| manganese | -0.00118 | 0.0001468 | -8.036 | 9.244e-16 | * * * |
| lead | 0.1461 | 0.04961 | 2.945 | 0.003232 | * * |
| zinc | 0.07303 | 0.009673 | 7.55 | 4.356e-14 | * * * |
| depth | om | gravel | clay | arsenic | cadmium | chromium | copper | iron | manganese | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| VIF | 1.51 | 1.58 | 1.03 | 1 | 2.2 | 3.27 | 4.02 | 5.68 | 2.85 | 3.1 | 4.27 | 8.11 |
## Analysis of Deviance Table
##
## Model 1: Bneo ~ depth + om + gravel + sand + clay + arsenic + cadmium +
## chromium + copper + iron + manganese + mercury + lead + zinc
## Model 2: Bneo ~ depth + om + gravel + clay + arsenic + cadmium + chromium +
## copper + iron + manganese + lead + zinc
## Resid. Df Resid. Dev Df Deviance
## 1 95 2443.9
## 2 97 2444.1 -2 -0.19436
Abundance of M. calcarea
## FULL MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.3
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 4.588 | 0.4109 | 11.17 | 5.907e-29 | * * * |
| depth | -0.009845 | 0.003206 | -3.07 | 0.002137 | * * |
| om | -0.3777 | 0.09957 | -3.793 | 0.0001487 | * * * |
| gravel | -2.593 | 0.7163 | -3.62 | 0.000294 | * * * |
| sand | -1.36 | 0.3342 | -4.068 | 4.738e-05 | * * * |
| clay | -0.01686 | 0.5468 | -0.03083 | 0.9754 | |
| arsenic | -0.231 | 0.09091 | -2.541 | 0.01105 | * |
| cadmium | -26.48 | 5.41 | -4.895 | 9.853e-07 | * * * |
| chromium | -0.02734 | 0.007081 | -3.861 | 0.0001131 | * * * |
| copper | -0.1341 | 0.05442 | -2.464 | 0.01373 | * |
| iron | -1.315e-06 | 3.155e-06 | -0.4169 | 0.6767 | |
| manganese | 0.0009874 | 0.0002701 | 3.656 | 0.0002564 | * * * |
| mercury | -22.68 | 7.502 | -3.023 | 0.002505 | * * |
| lead | -0.3859 | 0.1199 | -3.218 | 0.001289 | * * |
| zinc | 0.122 | 0.01902 | 6.414 | 1.413e-10 | * * * |
| depth | om | gravel | sand | clay | arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| VIF | 1.36 | 1.71 | 1.06 | 1.8 | 1.27 | 2.41 | 3.63 | 2.6 | 6.33 | 1.39 | 2.54 | 1.92 | 4.83 | 7.48 |
## REDUCED MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.3
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 4.561 | 0.3822 | 11.93 | 7.885e-33 | * * * |
| depth | -0.009956 | 0.003185 | -3.126 | 0.001775 | * * |
| om | -0.3808 | 0.09563 | -3.982 | 6.835e-05 | * * * |
| gravel | -2.581 | 0.7085 | -3.644 | 0.0002689 | * * * |
| sand | -1.381 | 0.2779 | -4.97 | 6.709e-07 | * * * |
| arsenic | -0.2346 | 0.09011 | -2.604 | 0.00922 | * * |
| cadmium | -26.14 | 5.322 | -4.91 | 9.093e-07 | * * * |
| chromium | -0.02785 | 0.006973 | -3.994 | 6.489e-05 | * * * |
| copper | -0.1348 | 0.05407 | -2.493 | 0.01266 | * |
| manganese | 0.0009644 | 0.000266 | 3.626 | 0.0002879 | * * * |
| mercury | -22.1 | 7.267 | -3.041 | 0.002355 | * * |
| lead | -0.3849 | 0.1193 | -3.225 | 0.001258 | * * |
| zinc | 0.1217 | 0.01886 | 6.455 | 1.082e-10 | * * * |
| depth | om | gravel | sand | arsenic | cadmium | chromium | copper | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| VIF | 1.35 | 1.64 | 1.05 | 1.5 | 2.38 | 3.58 | 2.56 | 6.28 | 2.49 | 1.86 | 4.81 | 7.43 |
## Analysis of Deviance Table
##
## Model 1: Mcal ~ depth + om + gravel + sand + clay + arsenic + cadmium +
## chromium + copper + iron + manganese + mercury + lead + zinc
## Model 2: Mcal ~ depth + om + gravel + sand + arsenic + cadmium + chromium +
## copper + manganese + mercury + lead + zinc
## Resid. Df Resid. Dev Df Deviance
## 1 96 613.58
## 2 98 613.76 -2 -0.1812
Abundance of E. parma
This species is not characteristic of BSI, so low abundances can be a problem.
## FULL MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.45
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 5.242 | 1.546 | 3.392 | 0.000694 | * * * |
| depth | 0.002041 | 0.009914 | 0.2058 | 0.8369 | |
| om | -2.607 | 0.5098 | -5.114 | 3.148e-07 | * * * |
| gravel | -4.339 | 2.102 | -2.064 | 0.03901 | * |
| sand | 2.573 | 1.12 | 2.297 | 0.02159 | * |
| clay | 2.36 | 5.038 | 0.4685 | 0.6394 | |
| arsenic | 0.2437 | 0.2089 | 1.167 | 0.2433 | |
| cadmium | -23.13 | 14.96 | -1.546 | 0.1222 | |
| chromium | 0.0586 | 0.03287 | 1.783 | 0.0746 | |
| copper | 0.4406 | 0.136 | 3.239 | 0.001199 | * * |
| iron | 3.668e-06 | 1.017e-05 | 0.3606 | 0.7184 | |
| manganese | -0.003072 | 0.001355 | -2.267 | 0.02336 | * |
| mercury | 51.59 | 15.64 | 3.299 | 0.0009687 | * * * |
| lead | 0.07575 | 0.3469 | 0.2184 | 0.8271 | |
| zinc | -0.1686 | 0.0623 | -2.706 | 0.006817 | * * |
| depth | om | gravel | sand | clay | arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| VIF | 1.37 | 1.44 | 1.22 | 2.28 | 1.14 | 1.89 | 3.35 | 4.48 | 4.91 | 1.63 | 3.44 | 2.88 | 4.96 | 7.46 |
## REDUCED MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.44
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 5.51 | 1.404 | 3.923 | 8.731e-05 | * * * |
| om | -2.662 | 0.4405 | -6.042 | 1.52e-09 | * * * |
| gravel | -4.147 | 1.979 | -2.096 | 0.03613 | * |
| sand | 2.356 | 0.999 | 2.358 | 0.01838 | * |
| cadmium | -22.1 | 12.03 | -1.836 | 0.06631 | |
| chromium | 0.03813 | 0.02042 | 1.867 | 0.06185 | |
| copper | 0.4162 | 0.1259 | 3.306 | 0.000945 | * * * |
| manganese | -0.001972 | 0.0009234 | -2.135 | 0.03274 | * |
| mercury | 52.51 | 12.94 | 4.057 | 4.97e-05 | * * * |
| zinc | -0.1436 | 0.05292 | -2.713 | 0.006658 | * * |
| om | gravel | sand | cadmium | chromium | copper | manganese | mercury | zinc | |
|---|---|---|---|---|---|---|---|---|---|
| VIF | 1.24 | 1.14 | 2.01 | 2.63 | 2.76 | 4.53 | 2.36 | 2.43 | 6.21 |
## Analysis of Deviance Table
##
## Model 1: Epar ~ depth + om + gravel + sand + clay + arsenic + cadmium +
## chromium + copper + iron + manganese + mercury + lead + zinc
## Model 2: Epar ~ om + gravel + sand + cadmium + chromium + copper + manganese +
## mercury + zinc
## Resid. Df Resid. Dev Df Deviance
## 1 96 152.92
## 2 101 155.25 -5 -2.3384
Abundance of Nematoda
This species is not characteristic of BSI, so low abundances can be a problem.
## FULL MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.63
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 0.319 | 0.478 | 0.6674 | 0.5045 | |
| depth | 0.01861 | 0.003137 | 5.933 | 2.983e-09 | * * * |
| om | -2.169 | 0.148 | -14.65 | 1.315e-48 | * * * |
| gravel | 4.004 | 0.3333 | 12.01 | 3.028e-33 | * * * |
| sand | 3.295 | 0.3576 | 9.214 | 3.136e-20 | * * * |
| clay | 1.027 | 1.555 | 0.6605 | 0.5089 | |
| arsenic | 0.985 | 0.05475 | 17.99 | 2.234e-72 | * * * |
| cadmium | -20.23 | 5.646 | -3.583 | 0.0003392 | * * * |
| chromium | 0.01349 | 0.00933 | 1.446 | 0.1481 | |
| copper | -0.1429 | 0.05585 | -2.559 | 0.01049 | * |
| iron | -4.467e-05 | 7.66e-06 | -5.831 | 5.508e-09 | * * * |
| manganese | -0.0004546 | 0.000324 | -1.403 | 0.1605 | |
| mercury | 32.59 | 6.515 | 5.003 | 5.646e-07 | * * * |
| lead | -1.644 | 0.1239 | -13.26 | 3.698e-40 | * * * |
| zinc | 0.1958 | 0.02238 | 8.748 | 2.175e-18 | * * * |
| depth | om | gravel | sand | clay | arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| VIF | 2.02 | 1.63 | 2.32 | 2.3 | 1.09 | 3.64 | 4.87 | 4.8 | 8.77 | 2.86 | 3.96 | 2.35 | 7.31 | 11.5 |
## REDUCED MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.63
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 0.3942 | 0.4644 | 0.8488 | 0.396 | |
| depth | 0.01855 | 0.003132 | 5.923 | 3.171e-09 | * * * |
| om | -2.172 | 0.1483 | -14.65 | 1.352e-48 | * * * |
| gravel | 3.953 | 0.3246 | 12.18 | 4.095e-34 | * * * |
| sand | 3.219 | 0.3388 | 9.499 | 2.123e-21 | * * * |
| arsenic | 0.9787 | 0.05382 | 18.19 | 6.757e-74 | * * * |
| cadmium | -20.51 | 5.626 | -3.646 | 0.000266 | * * * |
| chromium | 0.01395 | 0.009288 | 1.502 | 0.1332 | |
| copper | -0.1449 | 0.05572 | -2.6 | 0.009315 | * * |
| iron | -4.47e-05 | 7.65e-06 | -5.843 | 5.141e-09 | * * * |
| manganese | -0.0004526 | 0.0003238 | -1.398 | 0.1622 | |
| mercury | 31.78 | 6.386 | 4.977 | 6.457e-07 | * * * |
| lead | -1.632 | 0.1222 | -13.35 | 1.164e-40 | * * * |
| zinc | 0.1958 | 0.02239 | 8.746 | 2.204e-18 | * * * |
| depth | om | gravel | sand | arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| VIF | 2.02 | 1.63 | 2.26 | 2.17 | 3.58 | 4.85 | 4.78 | 8.75 | 2.85 | 3.96 | 2.3 | 7.22 | 11.5 |
## Analysis of Deviance Table
##
## Model 1: Nema ~ depth + om + gravel + sand + clay + arsenic + cadmium +
## chromium + copper + iron + manganese + mercury + lead + zinc
## Model 2: Nema ~ depth + om + gravel + sand + arsenic + cadmium + chromium +
## copper + iron + manganese + mercury + lead + zinc
## Resid. Df Resid. Dev Df Deviance
## 1 96 1438.9
## 2 97 1439.3 -1 -0.37093
Species richness
## FULL MODEL
## Adjusted R2 is: 0.19
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 20.89 | 4.908 | 4.255 | 4.853e-05 | * * * |
| depth | 0.05401 | 0.03024 | 1.786 | 0.07725 | |
| om | 1.049 | 0.8738 | 1.2 | 0.233 | |
| gravel | -0.202 | 4.225 | -0.04782 | 0.962 | |
| sand | 1.02 | 3.733 | 0.2732 | 0.7853 | |
| clay | -0.4441 | 3.874 | -0.1147 | 0.909 | |
| arsenic | 0.1496 | 0.6386 | 0.2342 | 0.8153 | |
| cadmium | -100.4 | 44.85 | -2.239 | 0.02745 | * |
| chromium | 0.0484 | 0.0826 | 0.5859 | 0.5593 | |
| copper | -0.2912 | 0.5598 | -0.5202 | 0.6041 | |
| iron | -9.849e-05 | 4.158e-05 | -2.369 | 0.01985 | * |
| manganese | -0.002435 | 0.002383 | -1.022 | 0.3094 | |
| mercury | -26.03 | 58.91 | -0.4419 | 0.6596 | |
| lead | 1.508 | 1.158 | 1.302 | 0.1959 | |
| zinc | 0.04078 | 0.21 | 0.1941 | 0.8465 |
| depth | om | gravel | sand | clay | arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| VIF | 1.33 | 1.98 | 1.07 | 2.03 | 1.15 | 2.22 | 2.8 | 3.15 | 6.34 | 1.45 | 2.91 | 1.8 | 4.75 | 7.49 |
## REDUCED MODEL
## Adjusted R2 is: 0.25
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 20.95 | 3 | 6.984 | 2.616e-10 | * * * |
| depth | 0.07349 | 0.02407 | 3.053 | 0.002862 | * * |
| cadmium | -67.45 | 24.81 | -2.718 | 0.007665 | * * |
| iron | -0.0001053 | 3.024e-05 | -3.481 | 0.0007266 | * * * |
| lead | 0.8049 | 0.386 | 2.085 | 0.03946 | * |
| depth | cadmium | iron | lead | |
|---|---|---|---|---|
| VIF | 1.1 | 1.6 | 1.09 | 1.64 |
## Analysis of Variance Table
##
## Model 1: S ~ depth + om + gravel + sand + clay + arsenic + cadmium + chromium +
## copper + iron + manganese + mercury + lead + zinc
## Model 2: S ~ depth + cadmium + iron + lead
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 96 2100.5
## 2 106 2168.3 -10 -67.791 0.3098 0.977
## RMSE for the full model: 5.052289
## RMSE for the reduced model: 4.642693
Total abundance
## FULL MODEL
## Adjusted R2 is: 0.05
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 163.5 | 81.07 | 2.017 | 0.04656 | * |
| depth | -0.8406 | 0.4889 | -1.72 | 0.08876 | |
| om | 3.534 | 14.16 | 0.2496 | 0.8034 | |
| gravel | 39.94 | 68.72 | 0.5812 | 0.5625 | |
| sand | 20.62 | 61.43 | 0.3357 | 0.7379 | |
| clay | -74.72 | 62.74 | -1.191 | 0.2367 | |
| arsenic | 4.502 | 10.34 | 0.4353 | 0.6643 | |
| cadmium | -1300 | 728.6 | -1.784 | 0.07762 | |
| chromium | 0.4344 | 1.335 | 0.3254 | 0.7456 | |
| copper | -8.75 | 9.16 | -0.9552 | 0.3419 | |
| iron | -0.0005995 | 0.0006716 | -0.8926 | 0.3743 | |
| manganese | -0.04376 | 0.03849 | -1.137 | 0.2584 | |
| mercury | -899.4 | 951.6 | -0.9452 | 0.3469 | |
| lead | 38.53 | 18.72 | 2.058 | 0.04232 | * |
| zinc | 1.324 | 3.453 | 0.3833 | 0.7023 |
| depth | om | gravel | sand | clay | arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| VIF | 1.32 | 1.98 | 1.08 | 2.05 | 1.16 | 2.22 | 2.8 | 3.14 | 6.4 | 1.45 | 2.91 | 1.8 | 4.73 | 7.56 |
## REDUCED MODEL
## Adjusted R2 is: 0.09
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 170 | 43.85 | 3.876 | 0.000185 | * * * |
| depth | -0.7761 | 0.3971 | -1.955 | 0.0533 | |
| cadmium | -773.9 | 406.7 | -1.903 | 0.05977 | |
| manganese | -0.05945 | 0.01982 | -3 | 0.003375 | * * |
| lead | 23.04 | 7.627 | 3.021 | 0.003169 | * * |
| depth | cadmium | manganese | lead | |
|---|---|---|---|---|
| VIF | 1.1 | 1.59 | 1.52 | 1.96 |
## Analysis of Variance Table
##
## Model 1: N ~ depth + om + gravel + sand + clay + arsenic + cadmium + chromium +
## copper + iron + manganese + mercury + lead + zinc
## Model 2: N ~ depth + cadmium + manganese + lead
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 95 542243
## 2 105 578171 -10 -35928 0.6295 0.7853
## RMSE for the full model: 83.17193
## RMSE for the reduced model: 75.35638
Shannon index
## FULL MODEL
## Adjusted R2 is: 0.36
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 2.186 | 0.4506 | 4.852 | 4.73e-06 | * * * |
| depth | 0.01003 | 0.002776 | 3.614 | 0.0004829 | * * * |
| om | 0.1624 | 0.08021 | 2.024 | 0.04574 | * |
| gravel | -0.2883 | 0.3878 | -0.7434 | 0.4591 | |
| sand | 0.1327 | 0.3427 | 0.3873 | 0.6994 | |
| clay | 0.6397 | 0.3556 | 1.799 | 0.07518 | |
| arsenic | -0.06008 | 0.05862 | -1.025 | 0.308 | |
| cadmium | -4.535 | 4.117 | -1.101 | 0.2734 | |
| chromium | -0.003811 | 0.007582 | -0.5026 | 0.6164 | |
| copper | -0.01353 | 0.05139 | -0.2634 | 0.7928 | |
| iron | -6.19e-06 | 3.817e-06 | -1.622 | 0.1081 | |
| manganese | 7.63e-05 | 0.0002187 | 0.3488 | 0.728 | |
| mercury | 0.225 | 5.408 | 0.04162 | 0.9669 | |
| lead | 0.0373 | 0.1063 | 0.3509 | 0.7265 | |
| zinc | 0.003476 | 0.01928 | 0.1803 | 0.8573 |
| depth | om | gravel | sand | clay | arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| VIF | 1.33 | 1.98 | 1.07 | 2.03 | 1.15 | 2.22 | 2.8 | 3.15 | 6.34 | 1.45 | 2.91 | 1.8 | 4.75 | 7.49 |
## REDUCED MODEL
## Adjusted R2 is: 0.4
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 2.398 | 0.2877 | 8.335 | 3.204e-13 | * * * |
| depth | 0.009826 | 0.002459 | 3.996 | 0.0001201 | * * * |
| om | 0.1437 | 0.04872 | 2.949 | 0.003929 | * * |
| clay | 0.4838 | 0.3047 | 1.588 | 0.1153 | |
| cadmium | -5.308 | 1.828 | -2.904 | 0.004493 | * * |
| iron | -8.055e-06 | 2.755e-06 | -2.924 | 0.004237 | * * |
| depth | om | clay | cadmium | iron | |
|---|---|---|---|---|---|
| VIF | 1.22 | 1.24 | 1.02 | 1.28 | 1.08 |
## Analysis of Variance Table
##
## Model 1: H ~ depth + om + gravel + sand + clay + arsenic + cadmium + chromium +
## copper + iron + manganese + mercury + lead + zinc
## Model 2: H ~ depth + om + clay + cadmium + iron
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 96 17.700
## 2 105 18.252 -9 -0.55204 0.3327 0.9621
## RMSE for the full model: 0.514536
## RMSE for the reduced model: 0.4369674
Piélou’s evenness
## FULL MODEL
## Adjusted R2 is: 0.28
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 0.7022 | 0.1567 | 4.48 | 2.061e-05 | * * * |
| depth | 0.002801 | 0.0009657 | 2.9 | 0.004621 | * * |
| om | 0.00709 | 0.0279 | 0.2541 | 0.8 | |
| gravel | -0.1254 | 0.1349 | -0.9297 | 0.3548 | |
| sand | -0.09292 | 0.1192 | -0.7794 | 0.4376 | |
| clay | 0.2574 | 0.1237 | 2.081 | 0.04009 | * |
| arsenic | -0.04734 | 0.02039 | -2.321 | 0.02239 | * |
| cadmium | 2.07 | 1.432 | 1.445 | 0.1517 | |
| chromium | -0.003906 | 0.002638 | -1.481 | 0.1419 | |
| copper | 0.0001094 | 0.01788 | 0.006118 | 0.9951 | |
| iron | 1.052e-06 | 1.328e-06 | 0.7924 | 0.4301 | |
| manganese | 0.0001575 | 7.61e-05 | 2.07 | 0.04111 | * |
| mercury | 0.3132 | 1.881 | 0.1665 | 0.8681 | |
| lead | -0.03207 | 0.03698 | -0.8674 | 0.3879 | |
| zinc | 5.44e-05 | 0.006707 | 0.008111 | 0.9935 |
| depth | om | gravel | sand | clay | arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| VIF | 1.33 | 1.98 | 1.07 | 2.03 | 1.15 | 2.22 | 2.8 | 3.15 | 6.34 | 1.45 | 2.91 | 1.8 | 4.75 | 7.49 |
## REDUCED MODEL
## Adjusted R2 is: 0.3
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 0.6259 | 0.0889 | 7.04 | 2.211e-10 | * * * |
| depth | 0.003258 | 0.0008167 | 3.989 | 0.0001244 | * * * |
| clay | 0.302 | 0.1102 | 2.741 | 0.007218 | * * |
| arsenic | -0.04566 | 0.01791 | -2.55 | 0.01224 | * |
| cadmium | 2.214 | 0.8719 | 2.539 | 0.01261 | * |
| chromium | -0.003954 | 0.00189 | -2.092 | 0.03889 | * |
| manganese | 0.0001903 | 4.996e-05 | 3.809 | 0.0002378 | * * * |
| lead | -0.02602 | 0.01894 | -1.374 | 0.1726 |
| depth | clay | arsenic | cadmium | chromium | manganese | lead | |
|---|---|---|---|---|---|---|---|
| VIF | 1.15 | 1.05 | 1.98 | 1.74 | 2.3 | 1.94 | 2.48 |
## Analysis of Variance Table
##
## Model 1: J ~ depth + om + gravel + sand + clay + arsenic + cadmium + chromium +
## copper + iron + manganese + mercury + lead + zinc
## Model 2: J ~ depth + clay + arsenic + cadmium + chromium + manganese +
## lead
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 96 2.1419
## 2 103 2.2114 -7 -0.069546 0.4453 0.8711
## RMSE for the full model: 0.175133
## RMSE for the reduced model: 0.1485803
Parameters
i) Simple regressions
These analyses have been do to explore the relationships between variables. As it is a huge number of results to interpret, only multiple regressions will be included in the article (see below).
| depth | om | gravel | sand | silt | clay | |
|---|---|---|---|---|---|---|
| Bneo | 0.02066 | 0.006557 | 0.000244 | 0.01557 | 0.05216 | -0.001626 |
| Mcal | -0.006558 | 0.003274 | 0.0002456 | 0.0004419 | -0.006683 | -0.007314 |
| Epar | 0.03402 | 0.1292 | -0.006223 | 0.179 | 0.1513 | -0.005043 |
| Nema | -0.007161 | 0.08987 | 0.05438 | 0.03268 | 0.07902 | -0.003509 |
| S | 0.1555 | -0.004351 | -0.002872 | 0.006156 | 0.003318 | -0.006916 |
| N | 0.02062 | 0.007067 | -0.0005827 | -0.002467 | -0.004443 | 0.004763 |
| H | 0.2897 | 0.03561 | -0.008062 | 0.0246 | 0.007538 | 0.006524 |
| J | 0.1198 | 0.02409 | -0.005515 | 0.006385 | -0.00433 | 0.02011 |
| depth | om | gravel | sand | silt | clay | |
|---|---|---|---|---|---|---|
| Bneo | 0.05883 | 0.1792 | 0.312 | 0.08696 | 0.00581 | 0.3737 |
| Mcal | 0.6673 | 0.2372 | 0.312 | 0.3063 | 0.6807 | 0.7617 |
| Epar | 0.02174 | 2.113e-05 | 0.6347 | 4.78e-07 | 4.035e-06 | 0.5426 |
| Nema | 0.7393 | 0.0003812 | 0.004948 | 0.02398 | 0.0008364 | 0.4545 |
| S | 2.915e-06 | 0.4996 | 0.4245 | 0.1853 | 0.2363 | 0.7074 |
| N | 0.05901 | 0.1717 | 0.3375 | 0.407 | 0.505 | 0.2085 |
| H | 4.833e-11 | 0.01935 | 0.9874 | 0.04369 | 0.1651 | 0.1797 |
| J | 4.26e-05 | 0.04539 | 0.576 | 0.1818 | 0.4984 | 0.06133 |
ii) Multiple regressions
To account for the high number of zeros in the characteristic species abundances, we used both Poisson and Zero-Inflated Poisson models for these regressions.
This table is summarizing the significative relationships with abiotic parameters as predictors, obtained with the AIC-reduced models from the multiple regressions below (ZIP not included)
| Predictor | Bneo | Mcal | Epar | Nema | S | N | H | J |
|---|---|---|---|---|---|---|---|---|
| depth | - | + | + | + | + | |||
| om | - | - | - | - | - | |||
| gravel | - | - | - | + | ||||
| sand | - | |||||||
| silt | - | + | + | |||||
| clay | - | - | + | + | ||||
| McFadden Pseudo-R2 | 0.21 | 0.04 | 0.42 | 0.45 | ||||
| Adjusted-R2 | 0.16 | 0.01 | 0.30 | 0.14 |
Abundance of B. neotena
## FULL MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.21
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 4.984 | 0.1049 | 47.49 | 0 | * * * |
| depth | -0.02219 | 0.00147 | -15.1 | 1.696e-51 | * * * |
| om | -0.1914 | 0.02967 | -6.45 | 1.121e-10 | * * * |
| gravel | -8.638 | 1.04 | -8.304 | 1.006e-16 | * * * |
| sand | -2.384 | 0.1329 | -17.95 | 5.224e-72 | * * * |
| clay | -6.552 | 0.5505 | -11.9 | 1.141e-32 | * * * |
| depth | om | gravel | sand | clay | |
|---|---|---|---|---|---|
| VIF | 1.03 | 1.42 | 1.02 | 1.42 | 1.07 |
## REDUCED MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.21
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 4.984 | 0.1049 | 47.49 | 0 | * * * |
| depth | -0.02219 | 0.00147 | -15.1 | 1.696e-51 | * * * |
| om | -0.1914 | 0.02967 | -6.45 | 1.121e-10 | * * * |
| gravel | -8.638 | 1.04 | -8.304 | 1.006e-16 | * * * |
| sand | -2.384 | 0.1329 | -17.95 | 5.224e-72 | * * * |
| clay | -6.552 | 0.5505 | -11.9 | 1.141e-32 | * * * |
| depth | om | gravel | sand | clay | |
|---|---|---|---|---|---|
| VIF | 1.03 | 1.42 | 1.02 | 1.42 | 1.07 |
## Analysis of Deviance Table
##
## Model 1: Bneo ~ depth + om + gravel + sand + clay
## Model 2: Bneo ~ depth + om + gravel + sand + clay
## Resid. Df Resid. Dev Df Deviance
## 1 119 3227.1
## 2 119 3227.1 0 0
## FULL MODEL (Zero-Inflated Poisson)
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | 3.512 | 0.07284 | 48.21 | 0 |
| depth | -0.03064 | 0.001526 | -20.08 | 1.133e-89 |
| om | -0.5021 | 0.04009 | -12.53 | 5.426e-36 |
| gravel | -3.35 | 0.9649 | -3.472 | 0.0005171 |
| silt | 2.555 | 0.1869 | 13.67 | 1.571e-42 |
| clay | -3.561 | 0.531 | -6.705 | 2.012e-11 |
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | 1.89 | 0.5951 | 3.176 | 0.001491 |
| depth | -0.0166 | 0.01513 | -1.097 | 0.2726 |
| om | -1.855 | 0.6182 | -3.001 | 0.002688 |
| gravel | -0.1986 | 2.515 | -0.07897 | 0.9371 |
| silt | -1.578 | 1.357 | -1.163 | 0.245 |
| clay | 2.841 | 1.983 | 1.433 | 0.152 |
## REDUCED MODEL
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | 3.512 | 0.07284 | 48.21 | 0 |
| depth | -0.03064 | 0.001526 | -20.08 | 1.133e-89 |
| om | -0.5021 | 0.04009 | -12.53 | 5.426e-36 |
| gravel | -3.35 | 0.9649 | -3.472 | 0.0005171 |
| silt | 2.555 | 0.1869 | 13.67 | 1.571e-42 |
| clay | -3.561 | 0.531 | -6.705 | 2.012e-11 |
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | 1.89 | 0.5951 | 3.176 | 0.001491 |
| depth | -0.0166 | 0.01513 | -1.097 | 0.2726 |
| om | -1.855 | 0.6182 | -3.001 | 0.002688 |
| gravel | -0.1986 | 2.515 | -0.07897 | 0.9371 |
| silt | -1.578 | 1.357 | -1.163 | 0.245 |
| clay | 2.841 | 1.983 | 1.433 | 0.152 |
Abundance of M. calcarea
## FULL MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.04
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 2.1 | 0.2266 | 9.268 | 1.89e-20 | * * * |
| depth | -0.0002055 | 0.002301 | -0.08931 | 0.9288 | |
| om | -0.2879 | 0.0709 | -4.06 | 4.907e-05 | * * * |
| gravel | -2.973 | 0.6931 | -4.289 | 1.792e-05 | * * * |
| sand | -0.2227 | 0.2539 | -0.8771 | 0.3804 | |
| clay | -0.4611 | 0.4535 | -1.017 | 0.3093 |
| depth | om | gravel | sand | clay | |
|---|---|---|---|---|---|
| VIF | 1.05 | 1.49 | 1.03 | 1.55 | 1.14 |
## REDUCED MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.04
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 1.909 | 0.07337 | 26.01 | 3.499e-149 | * * * |
| om | -0.2511 | 0.04814 | -5.216 | 1.833e-07 | * * * |
| gravel | -2.872 | 0.6858 | -4.188 | 2.82e-05 | * * * |
| om | gravel | |
|---|---|---|
| VIF | 1.01 | 1.01 |
## Analysis of Deviance Table
##
## Model 1: Mcal ~ depth + om + gravel + sand + clay
## Model 2: Mcal ~ om + gravel
## Resid. Df Resid. Dev Df Deviance
## 1 120 1078.1
## 2 123 1079.4 -3 -1.3235
## FULL MODEL (Zero-Inflated Poisson)
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | 3 | 0.1167 | 25.7 | 1.091e-145 |
| depth | -0.007223 | 0.002472 | -2.922 | 0.003483 |
| om | -0.3606 | 0.08189 | -4.403 | 1.067e-05 |
| gravel | -2.99 | 0.8165 | -3.662 | 0.0002505 |
| silt | -0.9106 | 0.3105 | -2.932 | 0.003364 |
| clay | 0.7077 | 0.4151 | 1.705 | 0.08823 |
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | 0.9476 | 0.5583 | 1.697 | 0.08966 |
| depth | -0.01665 | 0.01507 | -1.105 | 0.2692 |
| om | -0.8454 | 0.6339 | -1.334 | 0.1823 |
| gravel | 0.5623 | 2.24 | 0.251 | 0.8018 |
| silt | -1.634 | 1.33 | -1.229 | 0.2192 |
| clay | 3.328 | 1.913 | 1.739 | 0.08201 |
## REDUCED MODEL
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | 3 | 0.1167 | 25.7 | 1.091e-145 |
| depth | -0.007223 | 0.002472 | -2.922 | 0.003483 |
| om | -0.3606 | 0.08189 | -4.403 | 1.067e-05 |
| gravel | -2.99 | 0.8165 | -3.662 | 0.0002505 |
| silt | -0.9106 | 0.3105 | -2.932 | 0.003364 |
| clay | 0.7077 | 0.4151 | 1.705 | 0.08823 |
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | 0.9476 | 0.5583 | 1.697 | 0.08966 |
| depth | -0.01665 | 0.01507 | -1.105 | 0.2692 |
| om | -0.8454 | 0.6339 | -1.334 | 0.1823 |
| gravel | 0.5623 | 2.24 | 0.251 | 0.8018 |
| silt | -1.634 | 1.33 | -1.229 | 0.2192 |
| clay | 3.328 | 1.913 | 1.739 | 0.08201 |
Abundance of E. parma
Abundances are very low for this species.
## FULL MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.42
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 2.765 | 0.1565 | 17.67 | 7.629e-70 | * * * |
| depth | 0.002571 | 0.005288 | 0.4862 | 0.6268 | |
| om | -2.29 | 0.334 | -6.855 | 7.133e-12 | * * * |
| gravel | -5.524 | 1.272 | -4.341 | 1.419e-05 | * * * |
| silt | -2.361 | 0.5532 | -4.268 | 1.969e-05 | * * * |
| clay | 2.038 | 1.26 | 1.618 | 0.1057 |
| depth | om | gravel | silt | clay | |
|---|---|---|---|---|---|
| VIF | 1.15 | 1.35 | 1.03 | 1.22 | 1.1 |
## REDUCED MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.42
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 2.749 | 0.1526 | 18.02 | 1.426e-72 | * * * |
| om | -2.189 | 0.3093 | -7.079 | 1.45e-12 | * * * |
| gravel | -5.412 | 1.261 | -4.29 | 1.784e-05 | * * * |
| silt | -2.195 | 0.5615 | -3.909 | 9.283e-05 | * * * |
| om | gravel | silt | |
|---|---|---|---|
| VIF | 1.23 | 1.01 | 1.23 |
## Analysis of Deviance Table
##
## Model 1: Epar ~ depth + om + gravel + silt + clay
## Model 2: Epar ~ om + gravel + silt
## Resid. Df Resid. Dev Df Deviance
## 1 120 314.51
## 2 122 316.61 -2 -2.1088
## FULL MODEL (Zero-Inflated Poisson)
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | 2.891 | 0.2016 | 14.34 | 1.268e-46 |
| depth | -0.01208 | 0.00796 | -1.517 | 0.1292 |
| om | -1.264 | 0.3898 | -3.242 | 0.001188 |
| gravel | -2.964 | 1.284 | -2.309 | 0.02093 |
| silt | -0.7471 | 0.4346 | -1.719 | 0.08561 |
| clay | -0.5372 | 1.672 | -0.3212 | 0.748 |
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | -1.162 | 0.5966 | -1.948 | 0.05141 |
| depth | -0.002824 | 0.01584 | -0.1783 | 0.8585 |
| om | 1.522 | 0.9029 | 1.685 | 0.09194 |
| gravel | 1.491 | 2.53 | 0.5894 | 0.5556 |
| silt | 2.008 | 1.996 | 1.006 | 0.3143 |
| clay | -5.186 | 4.818 | -1.076 | 0.2817 |
## REDUCED MODEL
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | 2.764 | 0.1762 | 15.69 | 1.863e-55 |
| om | -1.428 | 0.3651 | -3.912 | 9.149e-05 |
| gravel | -3.484 | 1.357 | -2.567 | 0.01027 |
| silt | -0.875 | 0.4536 | -1.929 | 0.05375 |
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | -1.097 | 0.546 | -2.01 | 0.04446 |
| om | 1.537 | 0.7136 | 2.154 | 0.03122 |
| gravel | 1.3 | 2.473 | 0.5256 | 0.5992 |
| silt | 1.165 | 1.505 | 0.7741 | 0.4389 |
Abundance of Nematoda
Abundances are very low for this species.
## FULL MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.45
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 3.811 | 0.06576 | 57.95 | 0 | * * * |
| depth | 0.0209 | 0.001782 | 11.73 | 8.912e-32 | * * * |
| om | -2.976 | 0.1209 | -24.63 | 6.653e-134 | * * * |
| gravel | 1.322 | 0.1542 | 8.578 | 9.628e-18 | * * * |
| silt | 0.8836 | 0.1787 | 4.945 | 7.634e-07 | * * * |
| clay | -5.458 | 1.417 | -3.852 | 0.0001173 | * * * |
| depth | om | gravel | silt | clay | |
|---|---|---|---|---|---|
| VIF | 1.18 | 1.34 | 1.18 | 1.28 | 1.02 |
## REDUCED MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.45
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 3.811 | 0.06576 | 57.95 | 0 | * * * |
| depth | 0.0209 | 0.001782 | 11.73 | 8.912e-32 | * * * |
| om | -2.976 | 0.1209 | -24.63 | 6.653e-134 | * * * |
| gravel | 1.322 | 0.1542 | 8.578 | 9.628e-18 | * * * |
| silt | 0.8836 | 0.1787 | 4.945 | 7.634e-07 | * * * |
| clay | -5.458 | 1.417 | -3.852 | 0.0001173 | * * * |
| depth | om | gravel | silt | clay | |
|---|---|---|---|---|---|
| VIF | 1.18 | 1.34 | 1.18 | 1.28 | 1.02 |
## Analysis of Deviance Table
##
## Model 1: Nema ~ depth + om + gravel + silt + clay
## Model 2: Nema ~ depth + om + gravel + silt + clay
## Resid. Df Resid. Dev Df Deviance
## 1 120 2464.2
## 2 120 2464.2 0 0
## FULL MODEL (Zero-Inflated Poisson)
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | 3.957 | 0.06734 | 58.76 | 0 |
| depth | 0.01441 | 0.001915 | 7.525 | 5.263e-14 |
| om | -2.49 | 0.1439 | -17.31 | 4.257e-67 |
| gravel | 1.098 | 0.1574 | 6.978 | 2.986e-12 |
| silt | 1.034 | 0.1626 | 6.363 | 1.974e-10 |
| clay | -3.788 | 1.47 | -2.576 | 0.01 |
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | -1.343 | 0.5456 | -2.461 | 0.01387 |
| depth | -0.05033 | 0.01583 | -3.18 | 0.001472 |
| om | 2.196 | 0.6936 | 3.167 | 0.001542 |
| gravel | -0.6259 | 2.952 | -0.212 | 0.8321 |
| silt | 0.2631 | 1.622 | 0.1622 | 0.8711 |
| clay | -0.9465 | 3.245 | -0.2916 | 0.7706 |
## REDUCED MODEL
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | 3.957 | 0.06734 | 58.76 | 0 |
| depth | 0.01441 | 0.001915 | 7.525 | 5.263e-14 |
| om | -2.49 | 0.1439 | -17.31 | 4.257e-67 |
| gravel | 1.098 | 0.1574 | 6.978 | 2.986e-12 |
| silt | 1.034 | 0.1626 | 6.363 | 1.974e-10 |
| clay | -3.788 | 1.47 | -2.576 | 0.01 |
| Estimate | Std. Error | z value | Pr(>|z|) | |
|---|---|---|---|---|
| (Intercept) | -1.343 | 0.5456 | -2.461 | 0.01387 |
| depth | -0.05033 | 0.01583 | -3.18 | 0.001472 |
| om | 2.196 | 0.6936 | 3.167 | 0.001542 |
| gravel | -0.6259 | 2.952 | -0.212 | 0.8321 |
| silt | 0.2631 | 1.622 | 0.1622 | 0.8711 |
| clay | -0.9465 | 3.245 | -0.2916 | 0.7706 |
Species richness
## FULL MODEL
## Adjusted R2 is: 0.15
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 8.419 | 1.032 | 8.157 | 3.841e-13 | * * * |
| depth | 0.1088 | 0.02274 | 4.787 | 4.873e-06 | * * * |
| om | -0.8085 | 0.6478 | -1.248 | 0.2144 | |
| gravel | 4.139 | 3.77 | 1.098 | 0.2745 | |
| silt | 4.209 | 2.67 | 1.576 | 0.1175 | |
| clay | 1.003 | 3.42 | 0.2932 | 0.7699 |
| depth | om | gravel | silt | clay | |
|---|---|---|---|---|---|
| VIF | 1.02 | 1.54 | 1.09 | 1.59 | 1.07 |
## REDUCED MODEL
## Adjusted R2 is: 0.16
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 9.166 | 0.756 | 12.12 | 8.564e-23 | * * * |
| depth | 0.1082 | 0.02208 | 4.901 | 2.915e-06 | * * * |
| depth | |
|---|---|
| VIF | 1 |
## Analysis of Variance Table
##
## Model 1: S ~ depth + om + gravel + silt + clay
## Model 2: S ~ depth
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 120 2696.2
## 2 124 2760.6 -4 -64.401 0.7166 0.5822
## RMSE for the full model: 4.85609
## RMSE for the reduced model: 4.74687
Total abundance
## FULL MODEL
## Adjusted R2 is: 0.02
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 94.39 | 16.42 | 5.747 | 7.119e-08 | * * * |
| depth | -0.4541 | 0.3587 | -1.266 | 0.208 | |
| om | -13.69 | 10.16 | -1.348 | 0.1801 | |
| gravel | 75.9 | 59.1 | 1.284 | 0.2015 | |
| silt | 60.06 | 41.98 | 1.431 | 0.1552 | |
| clay | -50.95 | 53.63 | -0.95 | 0.344 |
| depth | om | gravel | silt | clay | |
|---|---|---|---|---|---|
| VIF | 1.02 | 1.54 | 1.09 | 1.59 | 1.07 |
## REDUCED MODEL
## Adjusted R2 is: 0.01
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 88.22 | 12.85 | 6.863 | 3.004e-10 | * * * |
| om | -15.98 | 9.33 | -1.713 | 0.08923 | |
| silt | 54.03 | 37.31 | 1.448 | 0.1501 |
| om | silt | |
|---|---|---|
| VIF | 1.4 | 1.4 |
## Analysis of Variance Table
##
## Model 1: N ~ depth + om + gravel + silt + clay
## Model 2: N ~ om + silt
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 119 656840
## 2 122 680015 -3 -23174 1.3995 0.2464
## RMSE for the full model: 76.2312
## RMSE for the reduced model: 75.91861
Shannon index
## FULL MODEL
## Adjusted R2 is: 0.29
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 1.26 | 0.09796 | 12.87 | 2.442e-24 | * * * |
| depth | 0.01491 | 0.002158 | 6.911 | 2.478e-10 | * * * |
| om | 0.03575 | 0.06148 | 0.5815 | 0.562 | |
| gravel | -0.06505 | 0.3578 | -0.1818 | 0.856 | |
| silt | 0.05329 | 0.2534 | 0.2103 | 0.8338 | |
| clay | 0.5161 | 0.3245 | 1.59 | 0.1144 |
| depth | om | gravel | silt | clay | |
|---|---|---|---|---|---|
| VIF | 1.02 | 1.54 | 1.09 | 1.59 | 1.07 |
## REDUCED MODEL
## Adjusted R2 is: 0.3
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 1.316 | 0.0723 | 18.2 | 1.049e-36 | * * * |
| depth | 0.01534 | 0.002093 | 7.328 | 2.695e-11 | * * * |
| clay | 0.5516 | 0.302 | 1.827 | 0.07019 |
| depth | clay | |
|---|---|---|
| VIF | 1 | 1 |
## Analysis of Variance Table
##
## Model 1: H ~ depth + om + gravel + silt + clay
## Model 2: H ~ depth + clay
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 120 24.285
## 2 123 24.568 -3 -0.28358 0.4671 0.7058
## RMSE for the full model: 0.4735333
## RMSE for the reduced model: 0.4516556
Piélou’s evenness
## FULL MODEL
## Adjusted R2 is: 0.14
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 0.6347 | 0.03476 | 18.26 | 1.914e-36 | * * * |
| depth | 0.003122 | 0.0007656 | 4.078 | 8.212e-05 | * * * |
| om | 0.02604 | 0.02181 | 1.194 | 0.2349 | |
| gravel | -0.1161 | 0.1269 | -0.9142 | 0.3624 | |
| silt | -0.06689 | 0.08991 | -0.744 | 0.4583 | |
| clay | 0.1838 | 0.1151 | 1.596 | 0.113 |
| depth | om | gravel | silt | clay | |
|---|---|---|---|---|---|
| VIF | 1.02 | 1.54 | 1.09 | 1.59 | 1.07 |
## REDUCED MODEL
## Adjusted R2 is: 0.14
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 0.6352 | 0.02572 | 24.69 | 1.692e-49 | * * * |
| depth | 0.003252 | 0.0007445 | 4.367 | 2.641e-05 | * * * |
| clay | 0.2309 | 0.1074 | 2.149 | 0.03357 | * |
| depth | clay | |
|---|---|---|
| VIF | 1 | 1 |
## Analysis of Variance Table
##
## Model 1: J ~ depth + om + gravel + silt + clay
## Model 2: J ~ depth + clay
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 120 3.0571
## 2 123 3.1099 -3 -0.052755 0.6903 0.5597
## RMSE for the full model: 0.1676339
## RMSE for the reduced model: 0.1598252
Metals
i) Simple regressions
These analyses have been do to explore the relationships between variables. As it is a huge number of results to interpret, only multiple regressions will be included in the article (see below).
| arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|
| Bneo | 0.02658 | 0.05792 | 0.03385 | 0.05284 | -0.007023 | -0.007612 | 0.01923 | 0.06944 | 0.09318 |
| Mcal | 0.04531 | 0.06456 | 0.03261 | 0.004907 | -0.007508 | 0.03006 | 0.06613 | 0.06284 | 0.01137 |
| Epar | 0.01663 | 0.03255 | 0.0243 | 0.02964 | 0.002643 | 0.02949 | -0.005137 | 0.02621 | 0.03627 |
| Nema | -0.009159 | 0.002577 | -0.005425 | 0.005019 | -0.003006 | 0.003156 | 0.0006913 | 0.00456 | 0.001428 |
| S | 0.01662 | 0.1027 | 0.118 | 0.05078 | 0.1085 | 0.07493 | 0.002283 | 0.03525 | 0.06309 |
| N | -0.006692 | -0.004822 | -0.008279 | -0.003719 | -0.001477 | -0.002075 | -0.008671 | 0.005467 | 0.005936 |
| H | 0.05214 | 0.1186 | 0.1572 | 0.09365 | 0.06617 | 0.0456 | 0.00858 | 0.086 | 0.1237 |
| J | 0.06716 | 0.02249 | 0.06068 | 0.07452 | -0.00309 | -0.0007157 | 0.004781 | 0.07601 | 0.08759 |
| arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|
| Bneo | 0.04787 | 0.006292 | 0.02968 | 0.008709 | 0.6304 | 0.6818 | 0.0784 | 0.003012 | 0.000658 |
| Mcal | 0.01413 | 0.004114 | 0.03219 | 0.2169 | 0.6719 | 0.03805 | 0.003723 | 0.004594 | 0.1352 |
| Epar | 0.09367 | 0.03233 | 0.05573 | 0.03912 | 0.2583 | 0.03952 | 0.5096 | 0.04909 | 0.02535 |
| Nema | 0.9675 | 0.2596 | 0.5251 | 0.2151 | 0.4147 | 0.2481 | 0.3019 | 0.2227 | 0.2844 |
| S | 0.09373 | 0.0003555 | 0.0001322 | 0.009938 | 0.000244 | 0.002121 | 0.2657 | 0.0271 | 0.004519 |
| N | 0.6052 | 0.4935 | 0.7563 | 0.4431 | 0.3621 | 0.3815 | 0.8161 | 0.2079 | 0.2008 |
| H | 0.009112 | 0.0001268 | 9.806e-06 | 0.0006383 | 0.003713 | 0.01387 | 0.1652 | 0.001044 | 9.084e-05 |
| J | 0.003486 | 0.0629 | 0.005274 | 0.002177 | 0.4179 | 0.3393 | 0.219 | 0.001979 | 0.0009426 |
ii) Multiple regressions
ZIP models are “computationally” singular, so they have not been computed here.
This table is summarizing the significative relationships with abiotic parameters as predictors, obtained with the AIC-reduced models from the multiple regressions below (ZIP not included)
| Predictor | Bneo | Mcal | Epar | Nema | S | N | H | J |
|---|---|---|---|---|---|---|---|---|
| arsenic | + | - | + | |||||
| cadmium | - | - | - | - | - | + | ||
| chromium | - | + | + | - | - | |||
| copper | - | - | + | - | - | |||
| iron | - | - | + | - | - | |||
| manganese | - | + | - | - | - | + | + | |
| mercury | + | - | + | |||||
| lead | - | + | - | + | + | - | ||
| zinc | + | - | - | |||||
| McFadden Pseudo-R2 | 0.29 | 0.35 | 0.21 | 0.27 | ||||
| Adjusted-R2 | 0.19 | 0.09 | 0.18 | 0.16 |
Abundance of B. neotena
## FULL MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.29
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 1.229 | 0.1704 | 7.209 | 5.618e-13 | * * * |
| arsenic | 0.04042 | 0.02611 | 1.548 | 0.1215 | |
| cadmium | -3.637 | 2.408 | -1.51 | 0.1309 | |
| chromium | -0.004222 | 0.005658 | -0.7462 | 0.4555 | |
| copper | -0.05152 | 0.02482 | -2.075 | 0.03795 | * |
| iron | -1.498e-05 | 5.514e-06 | -2.718 | 0.006574 | * * |
| manganese | -0.001245 | 0.0001363 | -9.134 | 6.574e-20 | * * * |
| mercury | 46.95 | 3.501 | 13.41 | 5.253e-41 | * * * |
| lead | 0.0005271 | 0.05816 | 0.009063 | 0.9928 | |
| zinc | 0.06668 | 0.009634 | 6.921 | 4.484e-12 | * * * |
| arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|
| VIF | 2.09 | 3.34 | 4.45 | 5.87 | 2.93 | 3.12 | 1.83 | 5.01 | 8.13 |
## REDUCED MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.29
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 1.243 | 0.1685 | 7.378 | 1.603e-13 | * * * |
| arsenic | 0.04415 | 0.0225 | 1.962 | 0.04981 | * |
| cadmium | -4.035 | 2.255 | -1.789 | 0.07361 | |
| copper | -0.0537 | 0.02417 | -2.221 | 0.02632 | * |
| iron | -1.559e-05 | 5.3e-06 | -2.941 | 0.003271 | * * |
| manganese | -0.001281 | 0.0001261 | -10.16 | 3.01e-24 | * * * |
| mercury | 46.59 | 3.163 | 14.73 | 4.105e-49 | * * * |
| zinc | 0.0649 | 0.008859 | 7.326 | 2.366e-13 | * * * |
| arsenic | cadmium | copper | iron | manganese | mercury | zinc | |
|---|---|---|---|---|---|---|---|
| VIF | 1.8 | 3.12 | 5.72 | 2.81 | 2.87 | 1.65 | 7.48 |
## Analysis of Deviance Table
##
## Model 1: Bneo ~ arsenic + cadmium + chromium + copper + iron + manganese +
## mercury + lead + zinc
## Model 2: Bneo ~ arsenic + cadmium + copper + iron + manganese + mercury +
## zinc
## Resid. Df Resid. Dev Df Deviance
## 1 100 2492.1
## 2 102 2492.7 -2 -0.56019
Abundance of M. calcarea
## FULL MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.35
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 3.353 | 0.3032 | 11.06 | 1.944e-28 | * * * |
| arsenic | -0.2509 | 0.1085 | -2.313 | 0.02075 | * |
| cadmium | -27.25 | 6.075 | -4.485 | 7.294e-06 | * * * |
| chromium | -0.02745 | 0.007202 | -3.812 | 0.0001378 | * * * |
| copper | -0.1298 | 0.06252 | -2.076 | 0.03789 | * |
| iron | -6.484e-06 | 3.214e-06 | -2.017 | 0.04365 | * |
| manganese | 0.001112 | 0.0002683 | 4.144 | 3.418e-05 | * * * |
| mercury | -14.97 | 8.212 | -1.823 | 0.06831 | |
| lead | -0.5097 | 0.141 | -3.615 | 0.0003005 | * * * |
| zinc | 0.1243 | 0.02138 | 5.816 | 6.016e-09 | * * * |
| arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|
| VIF | 2.39 | 3.48 | 2.29 | 6.41 | 1.37 | 2.36 | 1.87 | 4.78 | 7.07 |
## REDUCED MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.35
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 3.353 | 0.3032 | 11.06 | 1.944e-28 | * * * |
| arsenic | -0.2509 | 0.1085 | -2.313 | 0.02075 | * |
| cadmium | -27.25 | 6.075 | -4.485 | 7.294e-06 | * * * |
| chromium | -0.02745 | 0.007202 | -3.812 | 0.0001378 | * * * |
| copper | -0.1298 | 0.06252 | -2.076 | 0.03789 | * |
| iron | -6.484e-06 | 3.214e-06 | -2.017 | 0.04365 | * |
| manganese | 0.001112 | 0.0002683 | 4.144 | 3.418e-05 | * * * |
| mercury | -14.97 | 8.212 | -1.823 | 0.06831 | |
| lead | -0.5097 | 0.141 | -3.615 | 0.0003005 | * * * |
| zinc | 0.1243 | 0.02138 | 5.816 | 6.016e-09 | * * * |
| arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|
| VIF | 2.39 | 3.48 | 2.29 | 6.41 | 1.37 | 2.36 | 1.87 | 4.78 | 7.07 |
## Analysis of Deviance Table
##
## Model 1: Mcal ~ arsenic + cadmium + chromium + copper + iron + manganese +
## mercury + lead + zinc
## Model 2: Mcal ~ arsenic + cadmium + chromium + copper + iron + manganese +
## mercury + lead + zinc
## Resid. Df Resid. Dev Df Deviance
## 1 99 426.71
## 2 99 426.71 0 0
Abundance of E. parma
Abundances are very low for this species.
## FULL MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.21
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 4.382 | 1.018 | 4.306 | 1.661e-05 | * * * |
| arsenic | 0.2146 | 0.2492 | 0.861 | 0.3892 | |
| cadmium | -13.9 | 14.14 | -0.9828 | 0.3257 | |
| chromium | 0.0962 | 0.02354 | 4.087 | 4.376e-05 | * * * |
| copper | 0.3466 | 0.145 | 2.391 | 0.01681 | * |
| iron | 3.684e-05 | 1.088e-05 | 3.385 | 0.0007112 | * * * |
| manganese | -0.004212 | 0.001042 | -4.042 | 5.31e-05 | * * * |
| mercury | 33.95 | 10.83 | 3.136 | 0.001714 | * * |
| lead | 0.5873 | 0.275 | 2.136 | 0.03268 | * |
| zinc | -0.2496 | 0.062 | -4.027 | 5.657e-05 | * * * |
| arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|
| VIF | 1.89 | 2.95 | 3.34 | 5.36 | 1.57 | 3.01 | 1.6 | 3.65 | 7.05 |
## REDUCED MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.21
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 4.207 | 0.9844 | 4.274 | 1.923e-05 | * * * |
| chromium | 0.07753 | 0.0189 | 4.102 | 4.103e-05 | * * * |
| copper | 0.3992 | 0.1129 | 3.537 | 0.0004045 | * * * |
| iron | 3.684e-05 | 1.084e-05 | 3.399 | 0.0006771 | * * * |
| manganese | -0.003658 | 0.000816 | -4.483 | 7.377e-06 | * * * |
| mercury | 34.39 | 10.72 | 3.209 | 0.001332 | * * |
| lead | 0.5215 | 0.2177 | 2.396 | 0.01659 | * |
| zinc | -0.2632 | 0.05351 | -4.919 | 8.677e-07 | * * * |
| chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|
| VIF | 2.75 | 4.09 | 1.57 | 2.36 | 1.59 | 2.81 | 5.92 |
## Analysis of Deviance Table
##
## Model 1: Epar ~ arsenic + cadmium + chromium + copper + iron + manganese +
## mercury + lead + zinc
## Model 2: Epar ~ chromium + copper + iron + manganese + mercury + lead +
## zinc
## Resid. Df Resid. Dev Df Deviance
## 1 100 243.07
## 2 102 245.43 -2 -2.3615
Abundance of Nematoda
Abundances are very low for this species.
## FULL MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.27
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 4.014 | 0.1948 | 20.61 | 2.133e-94 | * * * |
| arsenic | 0.8225 | 0.03743 | 21.97 | 5.033e-107 | * * * |
| cadmium | -20.45 | 3.977 | -5.14 | 2.741e-07 | * * * |
| chromium | 0.1202 | 0.007634 | 15.75 | 7.36e-56 | * * * |
| copper | -0.05707 | 0.0249 | -2.292 | 0.0219 | * |
| iron | -4.905e-05 | 7.282e-06 | -6.735 | 1.64e-11 | * * * |
| manganese | -0.003388 | 0.0002613 | -12.97 | 1.912e-38 | * * * |
| mercury | 0.7612 | 4.554 | 0.1671 | 0.8673 | |
| lead | -0.4546 | 0.09573 | -4.749 | 2.048e-06 | * * * |
| arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | |
|---|---|---|---|---|---|---|---|---|
| VIF | 2.59 | 3.76 | 4.33 | 4.14 | 3.11 | 3.34 | 1.49 | 5.96 |
## REDUCED MODEL (Poisson)
## McFadden's Pseudo-R2 is: 0.27
| Estimate | Std. Error | z value | Pr(>|z|) | ||
|---|---|---|---|---|---|
| (Intercept) | 4.019 | 0.1924 | 20.9 | 5.881e-97 | * * * |
| arsenic | 0.8217 | 0.03716 | 22.11 | 2.544e-108 | * * * |
| cadmium | -20.37 | 3.95 | -5.157 | 2.504e-07 | * * * |
| chromium | 0.1201 | 0.007616 | 15.77 | 4.82e-56 | * * * |
| copper | -0.05756 | 0.02474 | -2.327 | 0.01997 | * |
| iron | -4.928e-05 | 7.137e-06 | -6.905 | 5.005e-12 | * * * |
| manganese | -0.003387 | 0.0002611 | -12.97 | 1.836e-38 | * * * |
| lead | -0.4499 | 0.09154 | -4.915 | 8.888e-07 | * * * |
| arsenic | cadmium | chromium | copper | iron | manganese | lead | |
|---|---|---|---|---|---|---|---|
| VIF | 2.57 | 3.74 | 4.32 | 4.11 | 3.05 | 3.33 | 5.7 |
## Analysis of Deviance Table
##
## Model 1: Nema ~ arsenic + cadmium + chromium + copper + iron + manganese +
## mercury + lead
## Model 2: Nema ~ arsenic + cadmium + chromium + copper + iron + manganese +
## lead
## Resid. Df Resid. Dev Df Deviance
## 1 101 2131.6
## 2 102 2131.6 -1 -0.027794
Species richness
## FULL MODEL
## Adjusted R2 is: 0.16
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 25 | 3.301 | 7.573 | 1.779e-11 | * * * |
| arsenic | 0.4272 | 0.6242 | 0.6845 | 0.4953 | |
| cadmium | -88.04 | 42.61 | -2.066 | 0.04139 | * |
| chromium | -0.02777 | 0.07971 | -0.3484 | 0.7283 | |
| copper | -0.2003 | 0.5601 | -0.3576 | 0.7214 | |
| iron | -9.051e-05 | 4.162e-05 | -2.175 | 0.03197 | * |
| manganese | -0.0008686 | 0.002235 | -0.3886 | 0.6984 | |
| mercury | -14.76 | 55.56 | -0.2656 | 0.7911 | |
| lead | 1.086 | 1.169 | 0.9292 | 0.355 | |
| zinc | 0.03835 | 0.211 | 0.1818 | 0.8561 |
| arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|
| VIF | 2.12 | 2.6 | 2.97 | 6.2 | 1.42 | 2.67 | 1.66 | 4.69 | 7.36 |
## REDUCED MODEL
## Adjusted R2 is: 0.19
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 25.98 | 2.603 | 9.98 | 5.648e-17 | * * * |
| cadmium | -85.3 | 25.03 | -3.408 | 0.0009242 | * * * |
| iron | -0.0001117 | 3.131e-05 | -3.567 | 0.0005413 | * * * |
| lead | 0.7594 | 0.4005 | 1.896 | 0.06063 |
| cadmium | iron | lead | |
|---|---|---|---|
| VIF | 1.56 | 1.09 | 1.63 |
## Analysis of Variance Table
##
## Model 1: S ~ arsenic + cadmium + chromium + copper + iron + manganese +
## mercury + lead + zinc
## Model 2: S ~ cadmium + iron + lead
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 101 2307.2
## 2 107 2359.0 -6 -51.726 0.3774 0.8919
## RMSE for the full model: 4.989739
## RMSE for the reduced model: 4.761062
Total abundance
## FULL MODEL
## Adjusted R2 is: 0.07
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 134.2 | 47.03 | 2.854 | 0.005261 | * * |
| arsenic | -2.777 | 8.863 | -0.3133 | 0.7547 | |
| cadmium | -1223 | 604.2 | -2.024 | 0.04569 | * |
| chromium | 0.9859 | 1.123 | 0.8776 | 0.3823 | |
| copper | -9.338 | 7.985 | -1.17 | 0.245 | |
| iron | -0.0005237 | 0.0005867 | -0.8926 | 0.3742 | |
| manganese | -0.04486 | 0.0315 | -1.424 | 0.1576 | |
| mercury | -879.8 | 785.1 | -1.121 | 0.2652 | |
| lead | 43.58 | 16.5 | 2.641 | 0.009615 | * * |
| zinc | 0.9465 | 3.013 | 0.3141 | 0.7541 |
| arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|
| VIF | 2.13 | 2.6 | 2.96 | 6.24 | 1.42 | 2.66 | 1.66 | 4.67 | 7.38 |
## REDUCED MODEL
## Adjusted R2 is: 0.09
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 122.9 | 31.97 | 3.844 | 0.0002088 | * * * |
| cadmium | -714.2 | 364.8 | -1.958 | 0.05293 | |
| copper | -4.688 | 3.175 | -1.476 | 0.1429 | |
| manganese | -0.04996 | 0.01833 | -2.725 | 0.007535 | * * |
| lead | 33.88 | 10.42 | 3.252 | 0.001545 | * * |
| cadmium | copper | manganese | lead | |
|---|---|---|---|---|
| VIF | 1.59 | 2.51 | 1.57 | 2.98 |
## Analysis of Variance Table
##
## Model 1: N ~ arsenic + cadmium + chromium + copper + iron + manganese +
## mercury + lead + zinc
## Model 2: N ~ cadmium + copper + manganese + lead
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 99 449178
## 2 104 461228 -5 -12050 0.5312 0.7522
## RMSE for the full model: 73.60588
## RMSE for the reduced model: 69.0653
Shannon index
## FULL MODEL
## Adjusted R2 is: 0.14
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 2.869 | 0.343 | 8.364 | 3.496e-13 | * * * |
| arsenic | 0.01789 | 0.06486 | 0.2759 | 0.7832 | |
| cadmium | -2.401 | 4.428 | -0.5422 | 0.5889 | |
| chromium | -0.01677 | 0.008283 | -2.024 | 0.04556 | * |
| copper | 0.004981 | 0.0582 | 0.0856 | 0.932 | |
| iron | -5.231e-06 | 4.324e-06 | -1.21 | 0.2292 | |
| manganese | 0.0003217 | 0.0002323 | 1.385 | 0.1691 | |
| mercury | 1.882 | 5.773 | 0.326 | 0.7451 | |
| lead | -0.05074 | 0.1214 | -0.4178 | 0.677 | |
| zinc | 0.003013 | 0.02193 | 0.1374 | 0.891 |
| arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|
| VIF | 2.12 | 2.6 | 2.97 | 6.2 | 1.42 | 2.67 | 1.66 | 4.69 | 7.36 |
## REDUCED MODEL
## Adjusted R2 is: 0.18
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 2.587 | 0.1636 | 15.81 | 7.149e-30 | * * * |
| chromium | -0.02062 | 0.004746 | -4.343 | 3.179e-05 | * * * |
| manganese | 0.0002977 | 0.0001483 | 2.008 | 0.04719 | * |
| chromium | manganese | |
|---|---|---|
| VIF | 1.74 | 1.74 |
## Analysis of Variance Table
##
## Model 1: H ~ arsenic + cadmium + chromium + copper + iron + manganese +
## mercury + lead + zinc
## Model 2: H ~ chromium + manganese
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 101 24.910
## 2 108 25.456 -7 -0.54588 0.3162 0.9452
## RMSE for the full model: 0.5485397
## RMSE for the reduced model: 0.4813905
Piélou’s evenness
## FULL MODEL
## Adjusted R2 is: 0.13
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 0.7812 | 0.1128 | 6.924 | 4.137e-10 | * * * |
| arsenic | -0.02017 | 0.02133 | -0.9456 | 0.3466 | |
| cadmium | 2.122 | 1.456 | 1.457 | 0.1481 | |
| chromium | -0.006769 | 0.002724 | -2.485 | 0.0146 | * |
| copper | 0.001312 | 0.01914 | 0.06857 | 0.9455 | |
| iron | 9.241e-07 | 1.422e-06 | 0.6498 | 0.5173 | |
| manganese | 0.0001934 | 7.639e-05 | 2.531 | 0.01291 | * |
| mercury | 1.178 | 1.899 | 0.6203 | 0.5365 | |
| lead | -0.05353 | 0.03994 | -1.34 | 0.1832 | |
| zinc | 0.001286 | 0.007211 | 0.1784 | 0.8588 |
| arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | |
|---|---|---|---|---|---|---|---|---|---|
| VIF | 2.12 | 2.6 | 2.97 | 6.2 | 1.42 | 2.67 | 1.66 | 4.69 | 7.36 |
## REDUCED MODEL
## Adjusted R2 is: 0.16
| Estimate | Std. Error | t value | Pr(>|t|) | ||
|---|---|---|---|---|---|
| (Intercept) | 0.8252 | 0.07737 | 10.67 | 1.757e-18 | * * * |
| cadmium | 1.949 | 0.9507 | 2.05 | 0.0428 | * |
| chromium | -0.00563 | 0.002017 | -2.792 | 0.006219 | * * |
| manganese | 0.0001854 | 5.368e-05 | 3.454 | 0.0007948 | * * * |
| lead | -0.04977 | 0.0168 | -2.962 | 0.00377 | * * |
| cadmium | chromium | manganese | lead | |
|---|---|---|---|---|
| VIF | 1.72 | 2.23 | 1.9 | 2 |
## Analysis of Variance Table
##
## Model 1: J ~ arsenic + cadmium + chromium + copper + iron + manganese +
## mercury + lead + zinc
## Model 2: J ~ cadmium + chromium + manganese + lead
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 101 2.6946
## 2 106 2.7561 -5 -0.061575 0.4616 0.804
## RMSE for the full model: 0.1765139
## RMSE for the reduced model: 0.1614341
4. Multivariate regressions
These analysis have been done on PRIMER, with a DistLM to identify the variables that explain the most the community variability and with a dbRDA to plot the results.
All abiotic variables at BSI
2017 dbRDA Design 2
Parameters
To be added!